Abstract 1379: Discovery of tumor-associated, immunogenic peptides presented in a patient-derived, mutant calreticulin-driven myeloproliferative neoplasm cell line
Authors: Najla Arshad, Nathalie Vigneron, Cansu Cimen Bozkus, Vincent Stroobant, Stefan Naulaerts, Nina Bhardwaj, Benoît Van den Eynde, Peter Cresswell
Journal: Cancer Research (2022)

Abstract Background: Myeloproliferative neoplasms (MPNs) are a type of chronic blood cancers. A subset are driven by frameshift mutations in the calreticulin gene (CALR). The CALR protein is a lectin chaperone and primarily assists in glycoprotein folding in the endoplasmic reticulum. It is also part of the peptide loading complex, a set of proteins involved in antigen processing and peptide presentation by major histocompatibility complex class I (MHC-I) molecules. All MPN-associated frameshift mutations in CALR lead to a similar change in its C-terminal, altering its protein-protein interactions. Examples include impaired chaperone activity of mutant CALR that impacts protein homeostasis and compromised activity of the MHC-I peptide loading complex. We hypothesized that these impaired functions will alter the repertoire of peptides presented by MHC-I in mutant CALR expressing cells, which we characterized in a patient-derived, mutant-CALR-driven myeloid tumor cell line, Marimo. Methods: We carried out an immunopeptidome analysis on Marimo cell line derivates expressing either wildtype or mutant CALR to identify potential MPN-associated peptides presented by MHC-I, and validated their immunogenicity in human samples. MHC-I-peptide complexes were immunoprecipitated from these Marimo cell line derivates, followed by peptide elution and analysis by mass spectrometry. A subset of peptides that were found in the mass spectrometry analysis of mutant CALR cells but not wildtype CALR cells were tested for their immunogenicity by assaying the in vitro T cell responses they evoked. Naïve T cells from healthy donors, carrying at least one MHC-I allele that matched the Marimo cells, were primed and expanded with the selected peptides and peptide-specific T cell responses were measured by intracellular staining detecting effector cytokines IFN-γ and TNF-α. Results: 1. The expression of mutant CALR disrupts the function of the peptide loading complex, leading to reduced recruitment of MHC-I and reducing its cell surface expression by almost 40% compared to cells expressing wildtype CALR. 2. Peptide repertoire of MHC-I is significantly altered by the expression of mutant CALR. Immunopeptidomics revealed a qualitative and quantitative difference in peptides presented by cells expressing wildtype CALR vs mutant CALR 3. The immunogenicity of a curated list of 24 peptides was tested in healthy donors, and at least 6 peptides activated T cell responses. Similar testing in MPN patients is planned. Conclusions: This is the first study to investigate the impact of mutant CALR on the repertoire of peptides presented by MHC-I in myeloid cells. We discovered tumor-associated, immunogenic peptides that may serve as potential targets of immunotherapy allowing the specific elimination of mutant CALR-expressing cells, which has been a challenge in the treatment of MPNs. Citation Format: Najla Arshad, Nathalie Vigneron, Cansu Cimen Bozkus, Vincent Stroobant, Stefan Naulaerts, Nina Bhardwaj, Benoît Van den Eynde, Peter Cresswell. Discovery of tumor-associated, immunogenic peptides presented in a patient-derived, mutant calreticulin-driven myeloproliferative neoplasm cell line [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1379.